GSM7799600: case0304-blood; Homo sapiens; Bisulfite-Seq
All patients underwent an incisional or Tru-Cut tumor biopsy prior to treatment. Tumor biopsies were snap-frozen in liquid nitrogen at removal and stored in liquid nitrogen, while WBC specimens were stored at –80°C after centrifugation of EDTA whole blood and plasma removal. Genomic DNA for methylation analyses was extracted from tumor and WBC samples using QIAamp DNA Mini kit (Qiagen, Valencia, CA). 500 ng of genomic DNA were bisulfite converted and subjected to BRCA1 gene promoter fragment amplification using four pairs of primers, that do not overlap with any of the CpG dinucleotides (GRCh38 genomic coordinates: CpG00–13 chr17:43125624–43126026, CpG14–31 chr17:43125270–43125640, CpG17–34 chr17:43125171–43125550, CpG33–49 chr17:43124861–43125249). All four amplicons were combined, indexed, and sequenced by 2x226 bp reads using Illumina MiSeq System (Illumina, San Diego, CA), resulting in an ultradeep coverage of about 30000x for each amplicon.